Minority Entrepreneurship and Innovation Pilot Program of 2006 - Directs the Administrator of the Small Business Administration to make grants to historically Black colleges and universities, Tribal Colleges, and Hispanic serving institutions, or to any entity formed by a combination of such institutions: (1) to assist in establishing an entrepreneurship curriculum for undergraduate or graduate studies; and (2) for the placement of small business development centers on the physical campus of the institution.

Requires an institution of higher education receiving a grant to: (1) develop a curriculum that includes training in various skill sets needed by successful entrepreneurs; and (2) open a small business development center.

Limits this pilot program to two fiscal years, and a grant to $1 million per fiscal year for any one institution of higher education.